By way of background, a number of industries are affected by regulations relating to water treatment, such as ballast water treatment systems (“BWTS”) on ships and the like. Such regulations require that microorganisms be effectively treated (killed) by the BWTS before such water is returned to the ocean or other body of water. Generally speaking, Zooplankton in the size range of approximately 10 to 50 microns is an “indicator” microorganism used to determine the effectiveness of treatment, though it will be appreciated that other organisms in alternative size ranges are possible depending on the context and other factors, such that organisms greater than 50 microns may also be the “indicators.” In the art, monitoring of the effectiveness of such BWTS has largely been handled through samples submitted to a lab, there most often involving human examination under a microscope. Such approaches to compliance assessment have numerous shortcomings in terms of accuracy, speed, and cost. Similarly, flow cytometry systems, though typically offering relatively higher throughput, are also lacking in terms of viability determination (determinations regarding whether an organism is living) and portability for field or deployed uses. Applicant has already made improvements over such prior art systems by developing new and novel evaluation systems for determining whether microorganisms are living, such as disclosed in pending international patent application Ser. No. PCT/US13/46334 filed Jun. 18, 2013, and U.S. provisional patent application Ser. No. 61/661,011 filed Jun. 18, 2012, to which the international application claims priority, both entitled “Microorganism Evaluation System.” The contents of the aforementioned applications are incorporated herein by reference.